Distribution of (CGG)n and FMR-1 associated microsatellite alleles in a normal Chilean population.

We report on the allele distribution in a normal Chilean population at 2 microsatellite loci neighbouring the FRAXA locus and at the CGG repeat in the 5' end of the FMR-1 gene, which causes the fragile X syndrome. The most common CGG repeat allele was 30 (41.7%), with 29 being second most common (30.2%). This distribution was similar from that seen in Caucasians but different from that observed in Chinese controls, where the most common allele was 29 repeats. Four alleles of FRAXAC1 and 6 of DXS548 were observed in the Chilean sample. A striking linkage disequilibrium of FMR-1 alleles with FRAXAC1 alleles was observed. In 90% of the 30 CGG repeat alleles only 31% of the 29 CGG repeat alleles had the FRAXAC1 154 bp allele. This result is in agreement with the suggestion that slippage between CGG repeat alleles 29 and 30 and between 152 and 154 FRAXAC1 alleles is very rare. This study suggests a founder chromosome effect in the Chilean population.

Purification of Escherichia coli chromosomal segments without cloning.

Pairs of genomic insertions made with elements carrying any one of several frequently used rare restriction sites allow physical purification of insertion delimited genes. However, native rare restriction sites can, either by causing (i) fragmentation of targeted intervals or (ii) generation of additional fragments that overlap electrophoretically with targeted ones, place severe limitations on this approach. We present a series of Escherichia coli mini-Tn10 insertions containing the rare-cutting polylinker 2 (RCP2) of rare restriction sites, which includes the 18-base-pair I-SceI site (absent from native E. coli sequences). Pulsed-field gel purification from RCP2 double insertion mutants of both an I-SceI fragment from strain K-12 (containing approximately 90-95 min) and an allelic I-SceI fragment from a pathogenic strain is demonstrated. The complete series of RCP2 insertions, containing different antibiotic resistances at intervals of approximately 35 kb in prototype K-12 strain MG1655, allows rapid purification of the genes from any E. coli chromosomal interval as an isolated I-SceI fragment.

New tools for integrated genetic and physical analyses of the Escherichia coli chromosome.

Genetic and biophysical techniques have traditionally been applied to genome mapping independently of one another. We present a series of Escherichia coli mini-Tn10 insertions that contain the rare-cutting polylinker 1 (RCP1) of rare restriction sites [including BlnI/AvrII, SpeI, NheI, XbaI, NotI, PacI and SfiI; Mahillon and Kleckner, Gene 116 (1992) 69-74] which allows them to be used not just for genetic mapping, but also for rapid physical mapping and integrated physical and genetic mapping of the E. coli chromosome. Their isolation and their physical and genetic coordinates in K-12 strain MG1655 are presented. Also, their use in purifying insertion-delimited DNAs from E. coli K-12 and in macrorestriction mapping of a pathogenic strain's chromosome is demonstrated. These insertions allow integration of (i) different macrorestriction patterns of a single strain's chromosome, (ii) the physical map of a single strain's chromosome with the genetic map of the species, and (iii) the physical maps of different strains' chromosomes.

Comparative genome mapping with mobile physical map landmarks.

We describe a method for comparative macrorestriction mapping of the chromosomes of Escherichia coli strains. In this method, a series of physically tagged E. coli K-12 alleles serve as mobile landmarks for mapping DNAs from other strains. This technique revealed evidence of strain-specific chromosomal additions or deletions in a pathogenic isolate and can be applied to most strains, yielding information on genealogy as well as virulence. In theory, the same strategy can be used to map and compare genomic DNAs from a wide variety of species.

Mini-Mu technology in Salmonella typhi: isolation of stable MudJ operon fusions by cis complementation.

This paper describes a method to achieve stable MudJ insertions in the Salmonella typhi Ty2 chromosome. The method is a modification of the genetic complementation system described previously for Salmonella typhimurium, which consists in placing the defective transposon (MudJ) near the transposase genes of a helper Mu phage on a single DNA fragment. This fragment is then introduced into a new bacterial host by means of P22 transduction. We constructed a S. typhi strain which carries MudJ and the Mu helper phage in the chromosome. This strain was induced to lytic growth and the lysate was used to infect S. typhi Ty2. The frequency of mutation was 2.0 x 10(-6) mutants per recipient bacterium. Superinfection with the Mu helper phage was about 1%. To determine the number of MudJ insertions, several mutants were subjected to Southern blot analysis. From a total of 25 mutants analyzed, only 4 contained more than one insertion. Our procedure compares well with the method described previously for the S. typhimurium-P22 system and can be applied to other Mu sensitive bacteria.

Mini-Mu technology in Salmonella typhi: isolation of stable MudJ operon fusions by cis complementation

This paper describes a method to achieve stable MudJ insertions in the Salmonella typhi Ty2 chromosome. The method is a modification of the genetic complementation system described previously for Salmonella typhimurium, which consists in placing the defective transposon (MudJ) near the transposase genes of a helper Mu phage on a single DNA fragment. This fragment is then introduced into a new bacterial host by means of P22 transduction. We constructed a S. typhi strain which carries MudJ and the Mu helper phage in the chromosome. This strain was induced to lytic growth and the lysate was used to infect S. typhi Ty2. The frequency of mutation was 2.0 x 10(-6) mutants per recipient bacterium. Superinfection with the Mu helper phage was about 1 percent. To determine the number of MudJ insertions, several mutants were subjected to Southern blot analysis. From a total of 25 mutants analyzed, only 4 contained more than one insertion. Our procedure compares well with the method described previously for the S. typhimurium-P22 system and can be applied to other Mu sensitive bacteria